Where to start?: How gene sequences shape translation initiation

Abstract

Proteins are essential drivers of virtually all cellular processes, and their timely and accurate production is critical for proper cell functioning. Protein synthesis is carried out by a molecular machine known as the ribosome, which decodes the genetic information contained in messenger RNA (mRNA) to produce proteins. Importantly, the ribosome does not translate the entire mRNA molecule, but rather a specific region known as the coding sequence (CDS). Accurate identification of the translation initiation codon by the ribosome, which marks the start of translation, is crucial. If the ribosome initiates translation at an incorrect initiation codon, it can result in the production of a protein with an altered amino acid sequence, which potentially could be harmful to the cell. While the process of start codon recognition is vital for cellular function, it is well established that it is not inherently efficient. The discovery of the Kozak consensus sequence revealed that certain nucleotide contexts around the initiation codon can significantly enhance the efficiency of initiation codon recognition. Since then, the Kozak sequence and derivative thereof have been considered the primary determinant of the efficiency of translation initiation. However, for many genes translation initiation occurs at initiation codons that are not surrounded by a Kozak consensus sequence. This raises important questions: How are these initiation codons efficiently recognized by ribosomes? Moreover, what role does the mRNA sequence surrounding the Kozak sequence perform in the initiation process? To address these questions, this dissertation describes the development and application of two novel fluorescent reporter systems designed to investigate initiation codon recognition with high precision. The first one, termed MashTag, is a reporter system that enables real-time visualization of translation with single-molecule resolution, simultaneously monitoring translation from canonical and alternative initiation codons within the same mRNA using fluorescent tags. This system demonstrates that initiation codon selection is not static; rather, it can fluctuate over time and differ between mRNAs with identical sequences. The second one, termed RiboScan, is a dual-color high-throughput reporter system designed to quantify the efficiency of start codon recognition across large numbers of mRNAs. The findings reveal that, in addition to the strength of the Kozak sequence, the mRNA sequence in close proximity to the Kozak sequence, both up- and downstream of the initiation codon, performs a substantial role in modulating translation initiation. These insights highlight a more intricate role of the mRNA sequence beyond the classical Kozak sequence in regulating translation initiation than previously acknowledged.